Stephen Fleming

Fix legacy 10x loader when more than one genome exists

3

Fixes #2246 A very small change with a small test. The new test fails for the current master branch, but passes with the fix.

read_10x_h5() `genome` argument appears recently broken for 10x v2 format

5

- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [x] (optional)...

Auto-generation of Study files for Single Cell Portal submission

5

I have recently been using `scanpy` to analyze my data and get it into a format that I want to share with others. I've been doing that using the Broad's...

sc.pl.dotplot() `standard_scale='var'`: should scaling be changed?

7

This issue references the following line of code: https://github.com/theislab/scanpy/blob/560bd5d348a502d5152eaf20f5f8bef794562a97/scanpy/plotting/_dotplot.py#L185 The documentation accurately describes the `standard_scale='var'` normalization strategy as "Whether or not to standardize the given dimension between 0 and 1,...

GPU memory overflow (leak?) for large datasets

12

We love scVI and use it all the time for batch-effect correction / dataset harmonization. As we scale to larger and larger datasets, we seem to have hit a wall...

Update FiveMinuteIntro: Java 11 requirement

1

I have ``` java version "1.8.0_172" Java(TM) SE Runtime Environment (build 1.8.0_172-b11) ``` and I was getting ``` Exception in thread "main" java.lang.UnsupportedClassVersionError: org/hsqldb/jdbcDriver has been compiled by a more...

## Details * Read the Docs project URL: https://cellbender.readthedocs.io/en/latest/ * Build URL (if applicable): https://readthedocs.org/projects/cellbender/builds/17259494/ * Read the Docs username (if applicable): https://readthedocs.org/profiles/sjfleming/ ## Expected Result The docs should render...

Do you implement the conditional version of the hypergeometric (Fisher’s exact) test that is implemented in GOstats 2.0 (described in Falcon and Gentleman, Bioinformatics, 2007)? https://pubmed.ncbi.nlm.nih.gov/17098774/ The last paragraph of...

# Description I believe this is a bug. I tried to use `stderr()` in the `output` section of a `workflow`, rather than the output section of a `task`. The resulting...

Support for python 3.10?

1

Hello! I love this package, thanks for writing it. I see that python 3.10 doesn't seem to be an option when installing from conda-forge. Is that right? Is there any...